Structure of PDB 6pjn Chain B Binding Site BS01

Receptor Information

>6pjn Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: OQP
• InChI: InChI=1S/C33H43N3O8/c1-41-32(40)36-33(15-8-9-16-33)30(38)34-24(18-22-10-4-2-5-11-22)20-27(37)26(19-23-12-6-3-7-13-23)35-31(39)44-28-21-43-29-25(28)14-17-42-29/h2-7,10-13,24-29,37H,8-9,14-21H2,1H3,(H,34,38)(H,35,39)(H,36,40)/t24-,25-,26-,27-,28-,29+/m0/s1
• InChIKey: RTQWXKCFXHCIFO-VEIVPZTASA-N
• SMILES:
  CACTVS 3.385: COC(=O)NC1(CCCC1)C(=O)N[CH](C[CH](O)[CH](Cc2ccccc2)NC(=O)O[CH]3CO[CH]4OCC[CH]34)Cc5ccccc5
  OpenEye OEToolkits 2.0.7: COC(=O)NC1(CCCC1)C(=O)NC(Cc2ccccc2)CC(C(Cc3ccccc3)NC(=O)OC4COC5C4CCO5)O
  CACTVS 3.385: COC(=O)NC1(CCCC1)C(=O)N[C@H](C[C@H](O)[C@H](Cc2ccccc2)NC(=O)O[C@H]3CO[C@H]4OCC[C@@H]34)Cc5ccccc5
  ACDLabs 12.01: C2(C1CCOC1OC2)OC(=O)NC(Cc3ccccc3)C(CC(Cc4ccccc4)NC(C5(CCCC5)NC(=O)OC)=O)O
  OpenEye OEToolkits 2.0.7: COC(=O)NC1(CCCC1)C(=O)N[C@@H](Cc2ccccc2)C[C@@H]([C@H](Cc3ccccc3)NC(=O)O[C@H]4CO[C@@H]5[C@H]4CCO5)O
• Formula: C33 H43 N3 O8
• Name: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3S,5S)-3-hydroxy-5-({1-[(methoxycarbonyl)amino]cyclopentane-1-carbonyl}amino)-1,6-diphenylhexan-2-yl]carbamate
• ChEMBL: CHEMBL4647359
• PDB chain: 6pjn Chain B Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6pjn Structural Analysis of Potent Hybrid HIV-1 Protease Inhibitors Containing Bis-tetrahydrofuran in a Pseudosymmetric Dipeptide Isostere.
• Resolution: 1.98 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 D30 G48 G49 I50 P81 V82
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 D30 G48 G49 I50 P81 V82
• Annotation score: 1
• Binding affinity: MOAD: Ki=7.3nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• Catalytic site (residue number reindexed from 1): D25 T26 G27
• Enzyme Commision number: 2.7.7.-
  2.7.7.49: RNA-directed DNA polymerase.
  2.7.7.7: DNA-directed DNA polymerase.
  3.1.-.-
  3.1.13.2: exoribonuclease H.
  3.1.26.13: retroviral ribonuclease H.
  3.4.23.16: HIV-1 retropepsin.

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:6pjn, PDBe:6pjn, PDBj:6pjn
• PDBsum: 6pjn
• PubMed: 32672965
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)